pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0197973

Loss of Fnip1 alters kidney developmental transcriptional program and synergizes with TSC1 loss to promote mTORC1 activation and renal cyst formation
Cited by: 17
Author(s): Ryan Michael Centini, Mark Tsang, Terri Iwata, Heon Park, Jeffrey J. Delrow, Daciana Margineantu, Brian M. Iritani, Haiwei Gu, H. Denny Liggitt, Janella Kang, Lim Kang, David M. Hockenbery, Daniel Raftery
Software Mentions: 2
Published: over 8 years ago

10.7554/eLife.48561

Id4 promotes the elimination of the pro-activation factor Ascl1 to maintain quiescence of adult hippocampal stem cells
Cited by: 52
Author(s): Isabelle Maria Blomfield, Brenda Rocamonde, M. Masdeu, Eskeatnaf Mulugeta, Stefania Vaga, Debbie Lc van den Berg, Emmanuelle Huillard, François Guillemot, Noelia Urbán
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0091353

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0098578

Digital Gene-Expression Profiling Analysis of the Cholesterol-Lowering Effects of Alfalfa Saponin Extract on Laying Hens
Cited by: 14
Author(s): Lu Zhou, Shi Ya, Rui Guo, Minggen Liang, Xiaoyan Zhu, Chengzhang Wang
Software Mentions: 2
Published: over 12 years ago

10.7717/peerj.2945

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
Cited by: 71
Author(s): William J. Brazelton, Christopher N Thornton, Alex Hyer, Katrina I. Twing, August Longino, Susan Q. Lang, Marvin D. Lilley, Gretchen L. Früh-Green, M. O. Schrenk
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0156453

Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin
Cited by: 41
Author(s): Jiayin Li, Xiaoya Tao, Li Li, Linchun Mao, Zisheng Luo, Zia Ullah Khan, Tiejin Ying
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.5103

Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation
Cited by: 9
Author(s): Bo Liu, Haode Wang, Zhoujie Ma, Xiaotong Gai, Yanqiu Sun, Shidao He, Xian Liu, Yanfeng Wang, Yue Xuan, Zhen Gao
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0116309

Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: over 11 years ago

10.1186/s12863-020-00843-5

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse
Cited by: 13
Author(s): Bei Li, Xiaolong He, Yiping Zhao, Ding Bai, Ming Du, Lianjie Song, Zhuang Liu, Zhenchen Yin, Manglai Dugarjaviin
Software Mentions: 2
Published: over 6 years ago

10.7554/eLife.44057

Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency
Cited by: 8
Author(s): Maxim V. C. Greenberg, Aurélie Teissandier, Marius Walter, Daan Noordermeer, Déborah Bourc’his
Software Mentions: 2
Published: over 7 years ago

10.1186/s12862-015-0581-0

Analysis of the erythropoietin of a Tibetan Plateau schizothoracine fish (Gymnocypris dobula) reveals enhanced cytoprotection function in hypoxic environments
Cited by: 26
Author(s): Qianghua Xu, Chi Zhang, Dongsheng Zhang, Huapeng Jiang, Syd S. Peng, Yang Liu, Kai Zhao, Congcong Wang, Liangbiao Chen
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0215472

UV-C treatment promotes quality of early ripening apple fruit by regulating malate metabolizing genes during postharvest storage
Cited by: 19
Author(s): Jakaria Chowdhury Onik, Yajing Xie, Yuquan Duan, Xiaojia Hu, Zhidong Wang, Qiong Lin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0244648

Transcriptomic analysis of the honey bee (Apis mellifera) queen spermathecae reveals genes that may be involved in sperm storage after mating
Cited by: 11
Author(s): Juliana Rangel, Tonya F. Shepherd, Alejandra González, Andrew Hillhouse, Kranti Konganti, Nancy H. Ing
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22063133

Transcriptome Analysis Unravels Key Factors Involved in Response to Potassium Deficiency and Feedback Regulation of K+ Uptake in Cotton Roots
Cited by: 10
Author(s): Dou-Dou Yang, Fangjun Li, Fei Yi, A. Egrinya Eneji, Xiaoli Tian, Zhaohu Li
Software Mentions: 2
Published: over 5 years ago

10.1186/s12862-018-1123-3

Widespread signatures of selection for secreted peptidases in a fungal plant pathogen
Cited by: 26
Author(s): Parvathy Krishnan, Xin Ma, Bruce A. McDonald, Patrick C. Brunner
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.10500

Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise
Cited by: 1
Author(s): Stela Mirla da Silva Felipe, Raquel Martins de Freitas, Emanuel Diego dos Santos Penha, Christina Pacheco, Daniel Freitas Freire Martins, Juliana Osório Alves, Paula Matias Soares, Adriano César Carneiro Loureiro, Tanes I. Lima, Leonardo R. Silveira, Alex Soares Marreiros Ferraz, Jorge Estefano Santana de Souza, José Henrique Leal-Cardoso, Denise Pires de Carvalho, Vânia Marilande Ceccatto
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0184974

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2
Cited by: 10
Author(s): Yadong Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.29702

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism
Cited by: 62
Author(s): William Putzbach, Quan Gao, Monal Patel, Stijn van Dongen, Ashley Haluck-Kangas, Aishe A. Sarshad, Elizabeth T. Bartom, Kwang Youn Kim, Denise M. Scholtens, Markus Hafner, Jonathan C. Zhao, Andrea E. Murmann, Marcus E. Peter
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0128350

Putative Regulatory Factors Associated with Intramuscular Fat Content
Cited by: 66
Author(s): A. S. M. César, Luciana Correia de Almeida Regitano, James E. Koltes, Eric R. Fritz-Waters, Dante Pazzanese Duarte Lanna, G. Gasparin, Gerson Barreto Mourão, P. S. N. Oliveira, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0179922

Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana)
Cited by: 21
Author(s): Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0179762

Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes
Cited by: 20
Author(s): Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Cheol Ho Sohn, Bethany Syracuse, Ευγενία Γιαννοπούλου, Sung Ho Park, Hee‐Ju Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias
Software Mentions: 2
Published: about 9 years ago

10.7717/peerj.2664

Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea
Cited by: 18
Author(s): Shijun Xiao, Panpan Wang, Linsong Dong, Yaguang Zhang, Zhaofang Han, Qiurong Wang, Zhiyong Wang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0156045

Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome
Cited by: 21
Author(s): Fei Yang, Cao H, Qingyang Xiao, Xiaomin Guo, Zhuang Yu, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Yan-Chun Song, Guoliang Hu, Ping Liu
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.2620

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
Cited by: 29
Author(s): Zhuo Huang, Si-Han Jin, Han-Du Guo, Xiao‐bo Zhong, Junlin He, Xi Li, Mingyan Jiang, Xiaofang Yu, Hai Long, Min Ma, Qibing Chen
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12862-021-01825-6

A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis
Cited by: 0
Author(s): Charlotte Lécureuil, Sophie Fouchécourt, Rémi Eliautout, Vanessa Guérin, Kévin Hidalgo, Dorian Neutre, Géraldine Roux, Philippe Monget
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.869

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols
Cited by: 24
Author(s): Peter A. Combs, Michael B. Eisen
Software Mentions: 2
Published: over 11 years ago

10.7717/peerj.8684

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity inC. elegans
Cited by: 10
Author(s): Charles Viau, Orçun Haçarız, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.11714

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
Cited by: 1
Author(s): Alex E. Mohr, Rebecca A. Reiss, Monique Beaudet, Johnny A. Sena, Jay S. Naik, Benjimen R. Walker, Karen L. Sweazea
Software Mentions: 2
Published: about 5 years ago

10.1186/s12969-019-0347-0

Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells
Cited by: 10
Author(s): Kaiyu Jiang, Rie Karasawa, Zihua Hu, Yanmin Chen, Lucy C Holmes, Kathleen M. O’Neil, James N. Jarvis
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0217343

Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling
Cited by: 6
Author(s): Lidia Hildebrand Pulz, Camila Neri Barra, Pâmela Almeida Alexandre, Greice Cestari Huete, Karine Germano Cadrobbi, Adriana Tomoko Nishiya, Sílvio Henrique de Freitas, Heidge Fukumasu, Ricardo de Francisco Strefezzi
Software Mentions: 2
Published: about 7 years ago

10.1186/s13071-018-3179-8

Transcriptomic insights into the early host-pathogen interaction of cat intestine with Toxoplasma gondii
Cited by: 8
Author(s): Meng Wang, Fu-Kai Zhang, Hany M. Elsheikha, Nian‐Zhang Zhang, Jun-Jun He, Jianxun Luo, Xingquan Zhu
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0241966

Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress
Cited by: 3
Author(s): Jessica Schmidt, Melissa Garcia, Chris Brien, Priyanka Kalambettu, Trevor Garnett, Delphine Fleury, Penny J. Tricker
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0165953

Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis)
Cited by: 32
Author(s): Zhuo Huang, Xiaojuan Zhong, Jun He, Si-Han Jin, Han-Du Guo, Xiaofang Yu, Yujue Zhou, Xi Li, Min Ma, Qibing Chen, Hai Long
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0143378

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos
Cited by: 9
Author(s): Rongping Zhang, Hehe Liu, Junying Liu, Jiwei Hu, Xiping Yan, Ding-min-cheng Wang, Liang Li, Jiwen Wang
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13071-017-1990-2

Transcriptomic responses of water buffalo liver to infection with the digenetic fluke Fasciola gigantica
Cited by: 23
Author(s): Fu-Kai Zhang, Xiaoxuan Zhang, Hany M. Elsheikha, Jun-Jun He, Zhao-An Sheng, Wei Zheng, Jian-Gang Ma, Weiyi Huang, Aijiang Guo, Xingquan Zhu
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.47791

Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1
Cited by: 59
Author(s): Anna E. Masser, Wenjing Kang, Joydeep Roy, Jayasankar Mohanakrishnan Kaimal, Jany Quintana-Cordero, Marc R. Friedländer, Claes Andréasson
Software Mentions: 2
Published: almost 7 years ago

10.1017/pao.2019.1

Effects of diethylcarbamazine and ivermectin treatment onBrugia malayigene expression in infected gerbils (Meriones unguiculatus)
Cited by: 6
Author(s): Morag MacLean, W. Walter Lorenz, Michael T. Dzimianski, Christopher Anna, Andrew R. Moorhead, Barbara J. Reaves, Adrian J. Wolstenholme
Software Mentions: 2
Published: over 7 years ago

10.3390/v12070713

Long Term Delta-9-tetrahydrocannabinol Administration Inhibits Proinflammatory Responses in Minor Salivary Glands of Chronically Simian Immunodeficieny Virus Infected Rhesus Macaques
Cited by: 7
Author(s): Xavier Álvarez, Karol Sestak, Siddappa N. Byrareddy, Mahesh Mohan
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0160970

Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination
Cited by: 17
Author(s): Iana H. Haralambieva, Michael T. Zimmermann, Inna G. Ovsyannikova, Diane E. Grill, Ann L. Oberg, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 2
Published: about 10 years ago

10.3390/v12060620

YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing
Cited by: 7
Author(s): Katarzyna Leskinen, Maria I. Pajunen, Miguel Vincente Gomez-Raya Vilanova, Saija Kiljunen, Andrew Nelson, Darren Smith, Mikael Skurnik
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-213X-13-12

Mef2A, a homologue of animal Mef2 transcription factors, regulates cell differentiation in Dictyostelium discoideum
Cited by: 7
Author(s): María Galardi-Castilla, Irene Fernandez-Aguado, Teresa Suárez, Leandro Sastre
Software Mentions: 2
Published: over 13 years ago

10.1016/j.stem.2020.10.018

Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate
Cited by: 94
Author(s): Henry De Belly, Aki Stubb, Akira Yanagida, Céline Labouesse, Philip H. Jones, Ewa K. Paluch, Kevin J. Chalut
Software Mentions: 2
Published: over 5 years ago

10.3390/v10040162

Deep Sequencing-Based Transcriptome Profiling Reveals Avian Interferon-Stimulated Genes and Provides Comprehensive Insight into Newcastle Disease Virus-Induced Host Responses
Cited by: 24
Author(s): Weiwei Liu, Xusheng Qiu, Song Chen, Yingjie Sun, Meng Chen, Ying Liao, Lei Tan, Zhuang Ding, Xiufan Liu, Chan Ding
Software Mentions: 2
Published: over 8 years ago

10.1080/21505594.2021.1972202

Role of intestinal extracellular matrix-related signaling in porcine epidemic diarrhea virus infection
Cited by: 3
Author(s): Yuchen Li, Jianda Li, Xiuyu Wang, Qingxin Wu, Qian Yang
Software Mentions: 2
Published: about 5 years ago

10.3390/cells8020112

Suppression of IgE-Independent Degranulation of Murine Connective Tissue-Type Mast Cells by Dexamethasone
Cited by: 10
Author(s): Keiko Yamada, Hitomi Sato, Kazuma Sakamaki, Mayumi Kamada, Yasushi Okuno, Nobuyuki Fukuishi, Kazuyuki Furuta, Satoshi Tanaka
Software Mentions: 2
Published: over 7 years ago

10.3390/cells10092403

Analysis of the Reversible Impact of the Chemodrug Busulfan on Mouse Testes
Cited by: 5
Author(s): Laura Thirouard, Hélène Holota, Mélusine Monrose, Manon Garcia, Angélique De Haze, Jean-Paul Saru, Françoise Caira, Claude Beaudoin, David H. Volle
Software Mentions: 2
Published: about 5 years ago

10.1186/s12860-018-0166-z

Novel roles for scleraxis in regulating adult tenocyte function
Cited by: 35
Author(s): Anne E. C. Nichols, Robert E. Settlage, Stephen R. Werre, Linda A. Dahlgren
Software Mentions: 2
Published: about 8 years ago

10.1080/21505594.2021.1936767

YhjC is a novel transcriptional regulator required for Shigella flexneri virulence
Cited by: 7
Author(s): Wanwu Li, Lingyan Jiang, Xiaoqian Liu, Rui Guo, Shuai Ma, Jingting Wang, Shuangshuang Ma, Shujie Li, Huiying Li
Software Mentions: 2
Published: about 5 years ago

10.1080/21505594.2019.1707957

Determination of antiviral action of long non-coding RNA loc107051710 during infectious bursal disease virus infection due to enhancement of interferon production
Cited by: 15
Author(s): Xing Huang, Yigang Xu, Qingyu Lin, Weilong Guo, Di Zhao, Chunmei Wang, Li Wang, Han Zhou, Yanping Jiang, Wen Cui, Xinyuan Qiao, Guangqiang Ma, Lijie Tang
Software Mentions: 2
Published: over 6 years ago

10.1080/21505594.2018.1514237

Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis
Cited by: 15
Author(s): Xian Sun, Lu Zhang, Jun Jiang, Mark Ng, Zhenling Cui, Juntao Mai, Sang Kyun Ahn, Jingqian Liu, Jinyu Zhang, Jun Liu, Yao Li
Software Mentions: 2
Published: almost 8 years ago

10.3390/cells10040736

Control of Protein and Energy Metabolism in the Pituitary Gland in Response to Three-Week Running Training in Adult Male Mice
Cited by: 3
Author(s): Christina Walz, Julia Brenmoehl, Nares Trakooljul, Antonia Noce, Caroline Caffier, Daniela Ohde, Martina Langhammer, Klaus Wimmers, Siriluck Ponsuksili, Andreas Hoeflich
Software Mentions: 2
Published: over 5 years ago

10.3390/vetsci6020036

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq
Cited by: 6
Author(s): Chandra Shekhar Pareek, Mateusz Sachajko, J. M. Jaśkowski, Magdalena Herudzińska, Mariusz T. Skowroński, Krzysztof Domagalski, Joanna Szczepanek, Urszula Czarnik, P. Sobiech, Dominika Wysocka, Mariusz Pierzchała, Ewa Poławska, Kamila Stepanow, Magdalena Ogłuszka, Edyta Juszczuk-Kubiak, Yaping Feng, Dibyendu Kumar
Software Mentions: 2
Published: over 7 years ago

10.3390/cells7060055

Nanopipettes as Monitoring Probes for the Single Living Cell: State of the Art and Future Directions in Molecular Biology
Cited by: 28
Author(s): Gonca Bülbül, Gepoliano Chaves, Olivier Joseph, Rıfat Emrah Özel, Nader Pourmand
Software Mentions: 2
Published: over 8 years ago

10.18632/aging.102273

Attenuated activation of the unfolded protein response following exercise in skeletal muscle of older adults
Cited by: 16
Author(s): Corey R. Hart, Zachary C. Ryan, Kyle T. Pfaffenbach, Surendra Dasari, Mojtaba Parvizi, Antigoni Z. Lalia, Ian R. Lanza
Software Mentions: 2
Published: about 7 years ago

10.1161/CIRCULATIONAHA.120.051171

Extracellular Tuning of Mitochondrial Respiration Leads to Aortic Aneurysm
Cited by: 48
Author(s): Jorge Oller, Enrique Gabandé‐Rodríguez, María Jesús Ruiz-Rodríguez, Gabriela Desdín-Micó, Juan Aranda, Raquel Rodrigues‐Díez, C Ballesteros-Martinez, Eva Blanco, Raquel Roldán-Montero, Pedro Acuña, Alberto Gil, Carlos Esteban Martín-López, J. Francisco Nistal, Christian L. Lino Cárdenas, Mark E. Lindsay, José Luis Martı́n-Ventura, Ana M. Briones, Juan Miguel Redondo, Marı́a Mittelbrunn
Software Mentions: 2
Published: over 5 years ago

10.1186/s13567-017-0456-z

RNA-seq comparative analysis of Peking ducks spleen gene expression 24 h post-infected with duck plague virulent or attenuated virus
Cited by: 17
Author(s): Lijun Tian, Anchun Cheng, Mingshu Wang, Renyong Jia, Qiao Yang, Ying Wu, Kunfeng Sun, Dekang Zhu, Shun Chen, Mafeng Liu, Xinxin Zhao, Xiaoyue Chen
Software Mentions: 2
Published: about 9 years ago

10.1186/s13148-018-0527-7

Vitamin C increases 5-hydroxymethylcytosine level and inhibits the growth of bladder cancer
Cited by: 41
Author(s): Peng Ding, Guangzhe Ge, Yanqing Gong, Yonghao Zhan, Shiming He, Bao Guan, Yifan Li, Ziying Xu, Han Hao, Zhisong He, Gengyan Xiong, Cuijian Zhang, Yue Shi, Yuanyuan Zhou, Weimin Ci, Xuesong Li, Liqun Zhou
Software Mentions: 2
Published: about 8 years ago

10.1186/s13567-014-0104-9

Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
Cited by: 25
Author(s): Bernardo Bello-Ortí, Vincent Deslandes, Yannick D. N. Tremblay, Josée Labrie, Kate J. Howell, Alexander W. Tucker, Duncan J. Maskell, Virginia Aragón, Mario Jacques
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13148-015-0057-5

Replicative senescence is associated with nuclear reorganization and with DNA methylation at specific transcription factor binding sites
Cited by: 50
Author(s): Sonja Hänzelmann, Fabian Beier, Eduardo Gade Gusmao, Carmen M. Koch, Sebastian Hummel, Iryna Charapitsa, Sylvia Joussen, Vladimı́r Beneš, Tim H. Brümmendorf, George Reid, Ivan G. Costa, Wolfgang Wagner
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms22083896

Prolyl 3-Hydroxylase 2 Is a Molecular Player of Angiogenesis
Cited by: 1
Author(s): Paola Pignata, Ivana Apicella, Valeria Cicatiello, Caterina Puglisi, Sara Magliacane Trotta, Remo Sanges, Valeria Tarallo, Sandro De Falco
Software Mentions: 2
Published: over 5 years ago

10.1016/j.clim.2015.05.020

Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders
Cited by: 84
Author(s): Pauline A. van Schouwenburg, Emma E Davenport, Anne‐Kathrin Kienzler, Ishita Marwah, Benjamin Wright, Mary Lucas, Tomas Malinauskas, Hilary C. Martin, Helen Lockstone, Jean‐Baptiste Cazier, Helen Chapel, Julian C. Knight, Smita Y. Patel
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41385-020-00348-5

IL-22 receptor signaling in Paneth cells is critical for their maturation, microbiota colonization, Th17-related immune responses, and anti-Salmonella immunity
Cited by: 33
Author(s): Stephen Gaudino, Michael Beaupre, Xun Lin, Preet Joshi, Sonika Rathi, Patrick A. McLaughlin, Cody Kempen, Neil K. Mehta, Onur Eskiocak, Brian Yueh, Richard S. Blumberg, Adrianus W. M. van der Velden, Kenneth R. Shroyer, Agnieszka B. Bialkowska, Semir Beyaz, Perikala V. Kumar
Software Mentions: 2
Published: over 5 years ago

10.1002/ctm2.221

Influence of oncogenic mutations and tumor microenvironment alterations on extranodal invasion in diffuse large B‐cell lymphoma
Cited by: 40
Author(s): Rong Shen, Pengpeng Xu, Nan Wang, Hongmei Yi, Lei Dong, Di Fu, Jinyan Huang, Huizhen Huang, Anne Janin, Shu Cheng, Li Wang, Wei‐Li Zhao
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12885-018-4304-y

RNA-Seq reveals the existence of a CDKN1C-E2F1-TP53 axis that is altered in human T-cell lymphoblastic lymphomas
Cited by: 7
Author(s): Pilar López-Nieva, Pablo Fernández-Navarro, Concepción Vaquero-Lorenzo, María Villa‐Morales, Osvaldo Graña‐Castro, María Ángeles Cobos-Fernández, José Luis López-Lorenzo, Pilar Llamas, Laura González-Sánchez, Isabel Sastre, Marina Pollán, Marcos Malumbres, Javíer Santos, José Fernández‐Piqueras
Software Mentions: 2
Published: over 8 years ago

10.1038/s42003-019-0334-5

Murine osteoclasts secrete serine protease HtrA1 capable of degrading osteoprotegerin in the bone microenvironment
Cited by: 16
Author(s): Nagahiro Ochiai, Yutaka Nakachi, Tomotaka Yokoo, Takahiro Ichihara, Tore Eriksson, Yuki Yonemoto, Takumi Kato, Hitoshi Ogata, Natsuko Fujimoto, Yasuhiro Kobayashi, Nobuyuki Udagawa, Shinsuke Kaku, Tomokazu Ueki, Yasushi Okazaki, Naoyuki Takahashi, Toshio Suda
Software Mentions: 2
Published: over 7 years ago

10.1016/j.ymthe.2018.08.023

Recombinant BCG Overexpressing phoP-phoR Confers Enhanced Protection against Tuberculosis
Cited by: 14
Author(s): Sang Kyun Ahn, Vanessa Tran, Andrea S. Leung, Mark Ng, Ming Li, Jun Liu
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41380-018-0260-9

SSRIs target prefrontal to raphe circuits during development modulating synaptic connectivity and emotional behavior
Cited by: 52
Author(s): Mariano Soiza-Reilly, Frank J. Meye, Jimmy Olusakin, Ludovic Telley, Emilie Petit, X Chen, Manuel Mameli, Denis Jabaudon, J-Y Sze, Patricia Gaspar
Software Mentions: 2
Published: almost 8 years ago

10.7554/eLife.43101

Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae
Cited by: 39
Author(s): Alok Arun, Susana M. Coelho, Akira F. Peters, Simon Bourdareau, Laurent Pérès, Delphine Scornet, Martina Strittmatter, Agnieszka P. Lipinska, Haiqin Yao, Olivier Godfroy, Gabriel J Montecinos, Komlan Avia, Nicolas Macaisne, Christelle Troadec, Abdelhafid Bendahmane, J. Mark Cock
Software Mentions: 2
Published: over 7 years ago

10.1186/s12885-021-08495-z

Osteopontin isoform c promotes the survival of cisplatin-treated NSCLC cells involving NFATc2-mediated suppression on calcium-induced ROS levels
Cited by: 5
Author(s): Jing Huang, Mu Hu, Huan Niu, Jing Wang, Shuanying Yang, Shan Cheng, Wei Ding
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-02123-z

Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury
Cited by: 27
Author(s): Anna Uryga, Mandy O.J. Grootaert, Abel Martin Garrido, Sebnem Oc, Kirsty Foote, Joel Chappell, Alison Finigan, Francesca Rossiello, Fabrizio d’Adda di Fagagna, Dimitra Aravani, Helle F. Jørgensen, Martin R. Bennett
Software Mentions: 2
Published: over 5 years ago

10.1002/1878-0261.12489

Identification of lnc <scp>RNA</scp> s associated with early‐stage breast cancer and their prognostic implications
Cited by: 39
Author(s): Arunagiri Kuha Deva Magendhra Rao, Krishna Patel, Suneetha Korivi Jyothiraj, Balaiah Meenakumari, Shirley Sundersingh, Velusami Sridevi, Thangarajan Rajkumar, Akhilesh Pandey, Aditi Chatterjee, Harsha Gowda, Samson Mani
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-021-01708-y

Insulin-like 3 affects zebrafish spermatogenic cells directly and via Sertoli cells
Cited by: 8
Author(s): Diego Crespo, Luiz H. C. Assis, Yu Ting Zhang, Diego Safian, Tomasz Furmanek, Kai Ove Skaftnesmo, Birgitta Norberg, Wei Ge, Yung Ching Choi, Marjo J. den Broeder, Juliette Legler, Jan Bogerd, Rüdiger Schulz
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-02541-z

Optimising PHBV biopolymer production in haloarchaea via CRISPRi-mediated redirection of carbon flux
Cited by: 13
Author(s): Lin Lin, Junyu Chen, Ruchira Mitra, Quanxiu Gao, Feiyue Cheng, Tong Xu, Zhenqiang Zuo, Hua Xiang, Jing Han
Software Mentions: 2
Published: about 5 years ago

10.1186/s13024-017-0212-x

Hexokinases link DJ-1 to the PINK1/parkin pathway
Cited by: 41
Author(s): David N. Hauser, Adamantios Mamais, Mary Anne Conti, Christopher T. Primiani, R. Ileng Kumaran, Allissa Dillman, Rebekah G. Langston, Alexandra Beilina, Joseph H. Garcia, Alberto Díaz‐Ruiz, Michel Bernier, Fabienne C. Fiesel, Xu Hou, Wolfdieter Springer, Yán Li, Rafael de Cabo, Mark Cookson
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.molmet.2018.11.010

Deletion of myeloid IRS2 enhances adipose tissue sympathetic nerve function and limits obesity
Cited by: 16
Author(s): Marie-Therese Rached, Steven Millership, Silvia Pedroni, Agharul I. Choudhury, Ana S.H. Costa, Darran G. Hardy, Justyna Glegola, Elaine E. Irvine, Colin Selman, Megan Woodberry, Vijay K. Yadav, Sanjay Khadayate, António Vidal-Puig, Samuel Virtue, Christian Frezza, Dominic J. Withers
Software Mentions: 2
Published: over 7 years ago

10.1016/j.ymgmr.2019.100531

Effectiveness of integrated interpretation of exome and corresponding transcriptome data for detecting splicing variants of genes associated with autosomal recessive disorders
Cited by: 9
Author(s): Mamiko Yamada, Hisato Suzuki, Yuichi Shiraishi, Kenjiro Kosaki
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms22094966

Novel Seleno-Aspirinyl Compound AS-10 Induces Apoptosis, G1 Arrest of Pancreatic Ductal Adenocarcinoma Cells, Inhibits Their NF-κB Signaling, and Synergizes with Gemcitabine Cytotoxicity
Cited by: 10
Author(s): Deepkamal Karelia, Sangyub Kim, Manoj K. Pandey, Daniel Plano, Shantu Amin, Junxuan Lü, Arun Sharma
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-01907-7

GmBTB/POZ promotes the ubiquitination and degradation of LHP1 to regulate the response of soybean to Phytophthora sojae
Cited by: 26
Author(s): Chuanzhong Zhang, Qun Cheng, Huiyu Wang, Hong Gao, Xin Fang, Xi Chen, Ming Zhao, Wanling Wei, Bo Song, Shanshan Liu, Jianzhong Wu, Shuzhen Zhang, Pengfei Xu
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-019-0284-y

Changes in long-range rDNA-genomic interactions associate with altered RNA polymerase II gene programs during malignant transformation
Cited by: 30
Author(s): Jeannine Diesch, Megan J. Bywater, Elaine Sanij, Donald P. Cameron, William Schierding, Natalie Brajanovski, Jinbae Son, Jirawas Sornkom, Nadine Hein, M. Evers, Richard B. Pearson, Grant A. McArthur, Austen R. D. Ganley, Justin M. O’Sullivan, Ross D. Hannan, Gretchen Poortinga
Software Mentions: 2
Published: over 7 years ago

10.1002/mgg3.270

Gene-centric analysis implicates nuclear encoded mitochondrial protein gene variants in migraine susceptibility
Cited by: 7
Author(s): Shani Stuart, Miles C. Benton, David Eccles, Heidi G. Sutherland, Larisa M. Haupt, Rodney Arthur Lea, Lyn R. Griffiths
Software Mentions: 2
Published: over 9 years ago

10.1038/s42003-021-02160-8

Genome of the fatal tapeworm Sparganum proliferum uncovers mechanisms for cryptic life cycle and aberrant larval proliferation
Cited by: 6
Author(s): Taisei Kikuchi, Mehmet Dayı, Vicky L. Hunt, Kenji Ishiwata, Atsushi Toyoda, Asuka Kounosu, Simo Sun, Y. Maeda, Yoko Kondo, Belkisyolé Alarcón de Noya, Óscar Noya, Satoshi Kojima, Toshiaki Kuramochi, Haruhiko Maruyama
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-01940-6

INPP4B protects from metabolic syndrome and associated disorders
Cited by: 7
Author(s): Manqi Zhang, Yasemin Ceyhan, Elena M. Kaftanovskaya, Judy L. Vasquez, Jean Vacher, Filip K. Knop, Lubov Nathanson, Alexander I. Agoulnik, Michael Ittmann, Irina U. Agoulnik
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-01297-2

Redundant type II cadherins define neuroepithelial cell states for cytoarchitectonic robustness
Cited by: 9
Author(s): Kou Hiraga, Yukiko Inoue, Junko Asami, Mayuko Hotta, Yuki Morimoto, Shoji Tatsumoto, Mikio Hoshino, Yasuhiro Go, Tohru Inoue
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12885-017-3983-0

A novel lncRNA-focus expression signature for survival prediction in endometrial carcinoma
Cited by: 49
Author(s): Meng Zhou, Zhao-Yue Zhang, Hengqiang Zhao, Siqi Bao, Jie Sun
Software Mentions: 2
Published: over 8 years ago

10.1186/s12915-021-00949-x

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
Cited by: 30
Author(s): Amit Blumberg, Yixin Zhao, Yi Huang, Noah Dukler, Edward J. Rice, Alexandra G. Chivu, Katie Krumholz, Charles G. Danko, Adam Siepel
Software Mentions: 2
Published: over 5 years ago

10.1002/mgg3.1115

Identification of novel differentially expressed genes in retinas of STZ‐induced long‐term diabetic rats through RNA sequencing
Cited by: 5
Author(s): Xindan Xing, Yan Jiang, Hanying Wang, Yuan Zhang, Tian Niu, Qing Yuan, Ching‐Yi Wang, Haiyan Wang, Kun Liu
Software Mentions: 2
Published: over 6 years ago

10.1016/j.dnarep.2019.06.006

The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair
Cited by: 14
Author(s): Michael Tellier, Ronald Chalmers
Software Mentions: 2
Published: about 7 years ago

10.1186/s12915-018-0543-2

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat
Cited by: 64
Author(s): Parvathy Krishnan, Lukas Meile, Clémence Plissonneau, Xin Ma, Fanny E. Hartmann, Daniel Croll, Bruce A. McDonald, Andrea Sánchez‐Vallet
Software Mentions: 2
Published: about 8 years ago

10.1093/dnares/dsz009

Analysis of an improved Cyanophora paradoxa genome assembly
Cited by: 32
Author(s): Dana C. Price, Ursula Goodenough, Robyn Roth, Jae‐Hyeok Lee, Thamali Kariyawasam, Marek Mutwil, Camilla Ferrari, Fabio Facchinelli, Steven Ball, Ugo Cenci, Cheong Xin Chan, Nicole Wagner, Hwan Su Yoon, Andreas Weber, Debashish Bhattacharya
Software Mentions: 2
Published: over 7 years ago

10.1093/dnares/dsaa015

Insights into the evolution of symbiosis gene copy number and distribution from a chromosome-scale Lotus japonicus Gifu genome sequence
Cited by: 30
Author(s): Nadia Kamal, Terry Mun, Dugald Reid, JL Lin, Turgut Yiğit Akyol, Niels Sandal, Torben Asp, Hideki Hirakawa, Jens Stougaard, Klaus Mayer, Shusei Sato, Stig Uggerhøj Andersen
Software Mentions: 2
Published: over 6 years ago

10.1016/j.dib.2015.12.049

Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice
Cited by: 7
Author(s): Cesare Lancini, Gaetano Gargiulo, Paul C.M. van den Berk, Elisabetta Citterio
Software Mentions: 2
Published: over 10 years ago

10.1016/j.dib.2018.09.038

Data on transcriptome profiling of circulating microRNAs in dairy cattle
Cited by: 0
Author(s): Kesavan Markkandan, Hyun-Joo Lim, Dong Jin Lee, In-gang Shin, Seung-il Yoo, Chang Gwon Dang, Chang Pyo Hong, Kung Ahn
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms22105294

Regulation of Oxalate Metabolism in Spinach Revealed by RNA-Seq-Based Transcriptomic Analysis
Cited by: 6
Author(s): Vijay Joshi, Arianne Penalosa, M. S. Joshi, Sierra Rodríguez
Software Mentions: 2
Published: over 5 years ago

10.1016/j.dib.2015.07.032

Data in support of genome-wide identification of lineage-specific genes within Caenorhabditis elegans
Cited by: 2
Author(s): Kun Zhou, Beibei Huang, Ming Zou, Di Lü, Shunping He, Guoxiu Wang
Software Mentions: 2
Published: about 11 years ago

10.1016/j.dib.2018.03.091

Transcriptome data of Prorocentrum donghaiense Lu under nitrogen and phosphorus limitation
Cited by: 1
Author(s): Jingjing Li, Wei Xia, Hongpo Dong, Linjian Ou
Software Mentions: 2
Published: over 8 years ago

10.1093/database/baaa081

CitrusKB: a comprehensive knowledge base for transcriptome and interactome of Citrus spp. infected by Xanthomonas citri subsp. citri at different infection stages
Cited by: 2
Author(s): Adriano Ferrasa, Mayara Mari Murata, Teresa Del Carmen Gabriel Cofre, Juliana S. Cavallini, Gustavo Peron, Maria H. M. Julião, José Belasque, Henrique Ferreira, M. I. T. Ferro, Rui Pereira Leite, Helen Alves Penha, Flávia M. S. Carvalho, Alessandro M. Varani, Roberto Hirochi Herai, Jesus Aparecido Ferro
Software Mentions: 2
Published: over 6 years ago

10.1093/database/baz115

Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer
Cited by: 31
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Dario Veneziano, Giovanni Nigita, Veronica Balatti, Carlo M. Croce, Alfredo Ferro, Alfredo Pulvirenti
Software Mentions: 2
Published: over 7 years ago

10.3390/molecules24173046

Next Generation Sequencing-Based Transcriptome Predicts Bevacizumab Efficacy in Combination with Temozolomide in Glioblastoma
Cited by: 5
Author(s): Alimu Adilijiang, Masaki Hashimoto, Yusuke Okuno, Kosuke Aoki, Fumiharu Ohka, Sachi Maeda, Kuniaki Tanahashi, Kazuya Motomura, Hiroyuki Shimizu, Junya Yamaguchi, Toshihiko Wakabayashi, Atsushi Natsume
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.05003

Systematic imaging reveals features and changing localization of mRNAs in Drosophila development
Cited by: 118
Author(s): Helena Jambor, Vineeth Surendranath, Alex T. Kalinka, Pavel Mejstřík, Stephan Saalfeld, Pavel Tomančák
Software Mentions: 2
Published: over 11 years ago

10.3390/molecules23081908

Comparative Transcriptomic Profiling to Understand Pre- and Post-Ripening Hormonal Regulations and Anthocyanin Biosynthesis in Early Ripening Apple Fruit
Cited by: 31
Author(s): Jakaria Chowdhury Onik, Xiaojia Hu, Qiong Lin, Zhidong Wang
Software Mentions: 2
Published: about 8 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071